Week 2 Lecture Prep

PRE-LECTURE ABOUT CLASS 2

SLIDES ABOUT PROFESSOR JACOBSON

-Question 1 When biological polymerase copies DNA, it makes about 1 mistake per million base pairs (1:10^6).Since the human genome has around 3.2 billion base pairs, that error rate would mean every time one of my cells divides, it would introduce over 3,000 mistakes if there weren’t any correction mechanisms. There’s a 3’-5’ exonuclease that catches and removes errors during DNA synthesis, and then the MutS repair system acts as a backup to fix any mismatches that slipped through afterward. Together, these mechanisms keep my genetic information stable across cell divisions.

-Question 2 The average human protein is about 345 amino acids long (roughly 1036 base pairs of DNA). Because the genetic code is redundant, there are approximately 3^345 different DNA sequences that could produce the same protein—an astronomically large number. However, most of these sequences don’t actually work well in practice. Some fold into secondary structures like hairpins that block the copying machinery.

SLIDES ABOUT DR.LEPROUST -Question 1 The method that’s most commonly used today is called the phosphoramidite method, or phosphoramidite chemistry. From what I learned, this technique was developed back in 1981 by a researcher named Caruthers, and it’s still the gold standard in the industry. It’s used for both the traditional column-based synthesis approach and the newer silicon-based platforms that companies are working with now.

-Question 2 Even though each individual base might attach with really high efficiency, small errors happen at every single step of the process. By the time you reach 200 nucleotides, the percentage of molecules that are perfect and full-length has fallen to around 37% or even lower.

-Question 3 When I think about the cumulative error rate logic, the probability of building a perfect 2000 base pair molecule one base at a time is essentially zero. That’s why in practice, when scientists need to manufacture long genes, they don’t try to synthesize them directly. Instead, they make shorter verified fragments (oligos) and then assemble those pieces together to build the full-length gene.

SLIDES ABOUT DR.CHURCH There are 10 amino acids that humans can’t make on their own and have to get from food -> Phenylalanine (F), Valine (V), Threonine (T), Tryptophan (W), Isoleucine (I), Methionine (M), Histidine (H), Arginine (R), Leucine (L), and Lysine (K). The “Lysine Contingency” is a weak biocontainment strategy because lysine is already essential to all animals.